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Check for non-symbolic alt alleles before left aligning in liftover #1909

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merged 1 commit into from
Aug 10, 2023
Merged

Check for non-symbolic alt alleles before left aligning in liftover #1909

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4 changes: 3 additions & 1 deletion src/main/java/picard/util/LiftoverUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,9 @@ protected static VariantContextBuilder reverseComplementVariantContext(final Var
private static boolean isIndelForLiftover(final VariantContext vc) {
final Allele ref = vc.getReference();
if (ref.length() != 1) {
return true;
//need to make sure the only other alleles are not all symbolic or spanning deletion
return vc.getAlternateAlleles().stream()
.anyMatch(a -> !a.isSymbolic() && !a.equals(Allele.SPAN_DEL));
}

return vc.getAlleles().stream()
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14 changes: 14 additions & 0 deletions src/test/java/picard/util/LiftoverVcfTest.java
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Expand Up @@ -381,6 +381,7 @@ public Iterator<Object[]> indelFlipData() {
final Allele RefT = Allele.create("T", true);
final Allele RefA = Allele.create("A", true);
final Allele RefAC = Allele.create("AC", true);
final Allele RefGT = Allele.create("GT", true);
final Allele RefC = Allele.create("C", true);
final Allele RefG = Allele.create("G", true);

Expand Down Expand Up @@ -621,6 +622,19 @@ public Iterator<Object[]> indelFlipData() {
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// a spanning deletion with a multibase reference (for example a multiallelic mnp which has be split), where the spanning deletion is the only alt
// AC, * --> GT, *
start = CHAIN_SIZE - 13;
stop = start + 1;

builder.start(start).stop(stop).alleles(CollectionUtil.makeList(RefAC, spanningDeletion));
result_builder.start(CHAIN_SIZE - stop + 1).stop(CHAIN_SIZE - start + 1).alleles(CollectionUtil.makeList(RefGT, spanningDeletion));
genotypeBuilder.alleles(builder.getAlleles());
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

builder.noGenotypes();
result_builder.noGenotypes();

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